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This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4774
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Package 686/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esATAC 1.33.0  (landing page)
Zheng Wei
Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025)
git_url: https://git.bioconductor.org/packages/esATAC
git_branch: devel
git_last_commit: 90d779d
git_last_commit_date: 2025-10-29 10:42:12 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR    ERROR  skipped

BUILD results for esATAC on nebbiolo1

To the developers/maintainers of the esATAC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esATAC.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: esATAC
Version: 1.33.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data esATAC
StartedAt: 2025-10-31 17:43:54 -0400 (Fri, 31 Oct 2025)
EndedAt: 2025-10-31 17:44:34 -0400 (Fri, 31 Oct 2025)
EllapsedTime: 40.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data esATAC
###
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* checking for file ‘esATAC/DESCRIPTION’ ... OK
* preparing ‘esATAC’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package ‘esATAC’ ...
** this is package ‘esATAC’ version ‘1.33.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c BedLine.cpp -o BedLine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c BedUtils.cpp -o BedUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ChrDivi.cpp -o ChrDivi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CutCountPre.cpp -o CutCountPre.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CutSiteCount.cpp -o CutSiteCount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c LibComplexQC.cpp -o LibComplexQC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SortBed.cpp -o SortBed.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_wrapper.cpp -o rcpp_wrapper.o
rcpp_wrapper.cpp: In function ‘int CutSiteCount_wrapper(Rcpp::List)’:
rcpp_wrapper.cpp:334:7: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable]
  334 |   int tmp_k;
      |       ^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c renamer.cpp -o renamer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c sam2bed.cc -o sam2bed.o
sam2bed.cc: In member function ‘int SamToBed::sam2bed(int, int, char**, int, bool, bool)’:
sam2bed.cc:125:16: warning: unused variable ‘xspm’ [-Wunused-variable]
  125 |     regmatch_t xspm[1];
      |                ^~~~
sam2bed.cc: In member function ‘int SamToBed::sam2bed_merge(int, int, char**, int, bool, bool, int, int, bool)’:
sam2bed.cc:294:16: warning: unused variable ‘xspm’ [-Wunused-variable]
  294 |     regmatch_t xspm[1];
      |                ^~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o esATAC.so BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /tmp/RtmpnkgQG8/Rinst5300b39e1679b/00LOCK-esATAC/00new/esATAC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘makeTxDbFromUCSC’ is not exported by 'namespace:GenomicFeatures'
Execution halted
ERROR: lazy loading failed for package ‘esATAC’
* removing ‘/tmp/RtmpnkgQG8/Rinst5300b39e1679b/esATAC’
      -----------------------------------
ERROR: package installation failed